X-com, Emperor of Snakes (Chapter next Thursday)
by Lighting wolf knight
Summary: Nathan Jones has been leading x com for years before being supposedly killed in battle, when X-com finds this commander is dead, another arrives from the future, supposedly ruling the aliens with his queen. When the elders bring aliens and enemies from the past, X com must learn if it can trust the Emperor. Viper x Viper king. Oc On hold. Chapters on Thursday
1. Rouge Viper

**Summary/Disclaimer: Time for the first chapter of King of Snakes. Enjoy the 900-word chapter. I don't own X com, Firaxis and Microsoft do.**

 **(X-Com flagship** _ **Avenger,**_ **command deck.)**

Central Officer Bradford was many things but a leader he was not, without the Commander, he wouldn't be able to retake the planet from the Aliens and ADVENT.

However, he didn't know what had happened to the Commander, last time they had stormed the location where they had assumed the leader of X-Com to be, they had only found a few bodies, a broken pod and signs of damage.

Little did he knew what had really happened to the leader of X-Com at this moment as the _Avenger_ flew through the air above one of its Allie's bases.

 **(Forest outside Washington.)**

Another Advent Trooper fell to the ground as the figure moved around the body, leaving a scorched forest and a trail of slain Advent soldiers.

"That's the 20th Advent Trooper I've run into… Ttthis… Is getting ridiculous…"

The figure muttered as he put his captured Beam Rifle on his back, the moonlight revealed the figure to be none other then a Viper, which was surprising not only because he was killing ADVENT forces.

But also, because it was a MALE Viper, one whose significance to the rest of the world could not be understated.

The Viper's forked tongue 'sniffed' the air, revealing 2 more Advent dropships and signifying more Reinforcements.

Alien reinforcements, the Viper sighed and drew his weapon before taking cover in the shade of a fallen tree.

"Back to the grind…. Ttthis… Would be easier…. If I had sssoldiers…"

The Viper hissed as his ocean blue eyes sighted a dropship as he fired.

 **(** _ **Avenger**_ **, command Deck.)**

Over a dozen soldiers, that had been the result of the battle for a Resistance Base.

Bradford had been watching the world map when one of the officers on the deck had spoken up.

"Sir, there's been an engagement in Washington, over 2 Advent soldiers have been reported K.I.A… It's a Viper, sir…."

The Lieutenant reported as Bradford turned to the monitor before issuing an order.

"On screen, satellite, CTV, a damn street camera if you have to, I want to see this…"

Bradford ordered as he looked at the screen which showed a Blue and White scaled Viper with some red scales on his head.

Bradford watched him snap the neck of an Advent Trooper with his tongue, he stabbed another with a knife as he turned back to the camera and hissed at it before slithering off screen, leaving a trail of dead enemy soldiers.

The roars of Mutons, the screeches of other Vipers and the sound of more dropships being dispatched could be heard in the background.

"You said this was in Washington?"

Bradford asked, watching this with interest, the Lieutenant nodded before Bradford made a decision in his mind at the moment.

"Send X-Ray team, tell them to capture that Viper alive if they can… a Viper fighting against Advent? This seems fishy…."

Bradford ordered as he looked at the images on the screen, something about the Viper made him seem… Familiar.

 **(Washington.)**

Xirrra Ge Samwe looked at the departing dropships before slithering into the battle with a squad of Advent troopers at her back, she had been dispatched as part of a reinforcement unit sent to capture an important unit.

She paused to examine a slain Sectoid, it smelt of poison, poison from another Viper, she looked up just in time to see an Advent trooper go flying over her head.

"How… Many… More of you… Are going to come….?"

Xirrra heard hissed from another Viper as he put his knife back on his armored chest as the Vipers stared each other down.

They were cut off by a dropship setting down, allowing the Male Viper to knock out Xirrra with a whip of his tale, he turned and slithered behind a tree.

"What the hell… These kills look like a horror movie! Who the hell did this, it can't be a viper, can it?"

One of the Humans stated, Xirrra hissed weakly as another human checked one of the bodies and then looked at a crashed Advent dropship.

"They were ambushed, some of these bodies don't look like they were able to even to get a shot off… They were killed by broken necks or stab wounds."

"Who… Are you…. Why are you here?"

X-Ray team heard as they looked to see the Viper they were looking for, he aimed his Beam Rifle at the chest of the Ranger in charge of the squad.

"Wow…. That Viper is real… Hey buddy, we're not going to hurt you… We just want to talk."

The man said as the Viper rolled his eyes, they didn't notice the Female Viper start to wake up.

"Do you know how many… People, I've slain by now? What makes you more trustworthy then this… Sssslime….?"

The Viper hissed, he was cut off by the sounds of engines flying over them.

The _Avenger_ had arrived to the battlefield.

 **Author notes**

 **Phew, first chapter done! Yes, I told you I would be updating this story, yes, I know there's a few Viper stories but this one will be different things in this story that makes it different. I Do not know when this story will be updated again, it might be Wednesday. Until then, Lighting Wolf out!**


	2. Reunion

**Summary/disclaimer: Time for another chapter of King of Snakes. Enjoy the 900-word chapter. I don't own X-Com, Firaxis, Microsoft and a few others do.**

 **(** _ **Avenger**_ **, 2 hours after ambush.)**

The Viper King woke up to the sound of something hitting glass, he grunted and rose to see Xirrra was hitting the glass with her tail and hissing.

"You're not going to open it by hitting it…. Idiot…"

He hissed, his head hurt and his physic powers felt dimmed, he felt at his neck and felt a collar on it.

"Terrific…. Just what I expected from thissss Day…."

He hissed before laying down to rest once more.

 **(** _ **Avenger**_ **bridge.)**

Bradford was speechless from what Shen and Dr. Tygan were telling him at the moment.

"Your telling me… That Viper is the Commander?"

Bradford asked, he looked back at the monitor to see the Viper was examining his surroundings while the Female Viper continued to try and escape and hissed at any who came near.

"Yes, Central Officer… I and Dr. Shen have done a few tests on the male Viper when X-Ray team secured them…. His brainwaves are jumbled and altered, but we do have a match for Commander Nathan…. He also appears to have a control unit, liked to other alien units and ADVENT themselves…. The Elders must have done experiments on him…. He's not the same anymore."

Dr. Tygan explained, Bradford turned back to the monitors, the Viper King appeared docile, but was studying every detail and taking mental notes.

Something the commander was known to do, Bradford turned back to Tygan to ask a question.

"Can we reverse…. The transformation?"

He asked, trying not to insult the man who he used to consider a great officer.

"No, the process is permanent, to try and reverse it would kill the commander… If you wish to speak to him, it does seem he still remembers English and a few other…. Human languages… But he does also speak a lot of the alien language as a result of the transformation."

Tygan muttered, that was all Bradford needed to hear and he left the bridge to go and talk to the commander.

 **(** _ **Avenger**_ **holding cells.)**

Xirrra had long since calmed down by the time Bradford entered the room, she coiled in the edge of her cage and hissed as Bradford walked up to the other cage. 

"Commander… Nathan, you remember who I am?"

Bradford asked, the Viper was silent but rose up on his tail, towering over Bradford, his tongue lapped at the air as he placed his hands on the glass.

"This is a waste of time…"

Bradford muttered before he heard a voice.

"Bradford… I remember you…. Where am I…. Lieutenant?"

Bradford heard Nathan ask, he didn't like the human name, it…. It didn't suit the form he was now.

He would look for something suitable later on, he closed his eyes and focused on speaking.

His body glowed red and a floating version of himself appeared outside the cell.

"What the hell did they do to you, commander?"

Bradford asked as the Viper chuckled.

"You can see what they did, old friend… And second, you're going to call me by my other name when I'm a snake…. Funny…"

Nathan muttered in annoyance, he was amused but still a bit annoyed.

"Because you are still human, Viper or not, you're still the leader of X-Com… The Resistance needs you."

Bradford explained, Nathan shook his head, looking the human officer in the eye.

"How long have you been leader without me, John?"

Nathan asked, his tail hit the floor at this, he could tell Bradford didn't want to answer, didn't want to admit what both of them knew.

"I am not the leader of X-Com… You are, old friend…. I will fight the Aliens… But I will do it in my own way…"

Nathan muttered, Bradford went to speak but Nathan shook his head. Xirrra listened to this in interest.

"I trained you in case this happened…. You want me because I am smart, you are smart as well… I can't be the face of the resistance, it would paint a target the size of Earth on you… And we both know they would never accept me like thissss…."

Nathan explained, he chuckled and slinked back to the edge of his cage.

"Welcome to the _Avenger_ then…"

Bradford stated before leaving the room, Nathan turned to Xirrra who looked at him.

"Now…. Who are you then…."

Nathan muttered, looking right into the eyes of the Viper Warrior.

 **(** _ **Avenger bridge**_ **.)**

"He's still as smart as before, so at least the Elders didn't make him stupider."

Bradford muttered to Dr. Tygan, he looked at the monitor and saw Nathan was looking at the monitor and right where he sat in the cell from before.

"He is right though, the resistance can't know he's inhuman now, it would ruin morale and make people think we could be allying with the Elders…"

Tygan stated, Bradford turned to the monitor to look, Nathan had a plan, Bradford knew it, he just had to find out what it was.

 **Author Notes**

 **Phew, another chapter done! Yes, I am sorry about this chapter taking a while, I had forgotten about this story for a while, won't happen again. As for Nathan? He has his own plans. I also made the commander a Viper since I've seen a few stories where it's a normal soldier. Next chapter will be next Tuesday. Until then, Lighting Wolf out!**


	3. Revelations

**Summary/disclaimer: Time for another chapter of King of Snakes. Enjoy the 1000-word chapter. I don't own X-Com, Firaxis, Microsoft and a few others do.**

 **(Old X-Com Base.)**

There were several advantages to Nathan's form that made him appreciate being a Viper King. It made him faster due to how fast the former X-Com Commander could move, it made him more silent as there was no footsteps to be tracked.

It made killing easier, as the Advent Troopers learned as Nathan stabbed, broke necks and strangled all of the soldiers.

"Sssso simple…."

Nathan hissed to himself as he pulled his Combat Knife from a dead Advent Captain and pulled the body from the console it was on.

"Where are the alien…. Troopsssss?"

Nathan wondered aloud, he had yet to see even a single Sectoid or Muton in the base…. He remembered something from Dr. Valhen… Something about being able to command aliens with his psionic powers.

He wondered what happened to the Doctor…. He was fond of her, just like the other soldiers of X-Com…. But they couldn't be led by him, he would just complicate things.

He was about to type in commands when he heard a hiss behind him, he drew his Beam Pistol and turned to see Xirrra standing in the doorway.

"How did you…."

Nathan asked before Xirrra put her Plasma Rifle on her back, Nathan turned back to the console.

"Why… Fight… Elders?"

She asked as she slithered up to the console, Nathan ignored her and typed in commands.

"Why?"

She asked, her voice was curious, like a child, not angry, he turned to face her, his hood hid part of his face.

"They are monsterssssss…. Xirrra, they would hunt us to the last…. They destroyed Mankind…. And yet I will fight…"

Nathan hissed before Xirrra slithered closer, Nathan poked her back with his tail, he was getting off feelings around her… He cursed this.

Xirrra placed a hand on his chest, Nathan was forced back and it hit a button on the panel.

"What?"

Xirrra asked as she turned to look at the screen, it showed X-Com footage of the last war.

She saw Mutons… Before the mutations, Sectoids, Thin Men…. Her male counterpart.

And then she saw Elder Battleships, bombarding the cities, slaughtering dozens of Humans, they weren't even fighting, just fleeing.

"The Elders…."

Xirrra said as the video footage continued, it showed X-Com soldiers fighting valiantly against the Aliens, some were taken prisoner but weren't harmed.

Xirrra heard they killed ruthlessly, gunned down any in their way… This wasn't what she had heard.

All the blood that was being spilt, all of it, because the Aliens tried to force Mankind to surrender… And X-Com had tried in vain to stop it.

"What issss… Thissss?"

Xirrra asked, Insurgent Propaganda? No, that had been… Years ago… Before she had even been deployed here.

"Monsterssssss…. As I've said… That is what the Elders did, Xirrra… That is what they will do if we resist…."

Nathan said as he climbed to his… Tail, Xirrra's advance on him had knocked him to the ground.

Then a video had started to play, an old one, but one locked to the Commander himself.

"Commander… This is Dr. Valhen… If you're getting this, X-Com has fallen…. I've recorded this video after your… Upgrades… I know I've turned you into something… Inhuman, but Humanity needed someone who could fight like the Aliens… And who was smart enough to lead another uprising… I've unlocked three major advances in the old HQ…"

The recording said, Nathan was flabbergasted.

"She…. Knew this would happen…"

Nathan said, Valhen was even smarter then he thought, the recording continued.

"One was the Alien Battleship from Operation Slingshot… It's in a closed off hanger, it should still fly…. The second was A list of Human recruits, they were possible recruits for X-Com, but didn't match our specs… The third is…. I and Dr. Shen, had tried to create a way to make more advanced soldiers… Aliens on our side… I've found no better... And more ethical way… Then to clone them… I've moved the device to the Battleship…. I'm Sorry for making you what you are commander… But with your Viper Biology, combined with your powers and mind, the Aliens can be beaten… If you have more questions, the Battleship has more recordings… Godspeed, commander."

The recording said before it vanished, Nathan started to type in commands.

"You were… Created?"

Xirrra asked, she scolded herself, enough with the slow speaking and enough of her slow thoughts, she was a soldier.

"Modified… Dr. Valhen found me… And turned me to thissss…. Irreversible…. I've forgotten about the battleship…"

Nathan hissed as Xirrra nodded, Nathan pulled up the schematics for the base, a secret hanger which only the top brass of X-Com would know about.

"Bingo…."

Nathan stated before slithering off, he felt weight on his tail before turning to see Xirrra behind him.

"Coming… With you…"

Xirrra hissed, Nathan grunted but nodded, if she was persistent enough to follow him here, then she was persistent enough not to let him go.

"Keep… Up…"

Nathan hissed before vanishing through a door, Xirrra looked at her armor before hissing and smashing the ADVENT logo on it.

"Find… Truth…."

She said before she vanished, if ADVENT had used her… And the Elders, they would pay… She didn't know if they had… But she would find out.

"Nathan…."

She said, trying to get a taste for the name it didn't feel right… But she felt… Content by his side… Strange for her.

But it also felt right… And she took comfort in that…

 **Author Notes**

 **Phew, another chapter done! Yes, I'm returning to this story… As for Nathan and Xirrra? She will be the female protagonist of the story… As for the cloning and stuff? It will play into Nathan being a 'Emperor'… I also want to point out chapters for this story will be moved to Monday. Next chapter will be next week and will show Nathan and Xirrra making an army and setting out on their mission to defeat ADVENT and the Elders… Until then, Lighting Wolf out!**


	4. Building a army

**Summary/disclaimer: Time for another chapter of King of Snakes. Enjoy the 900-word chapter. I don't own X-Com, Firaxis, Microsoft and a few others do.**

 **(Alien Battleship, 2 hours later.)**

Nathan hadn't expected Mutons to be able to created so fast, the 10 or so around him surprised him, they were filed away into the cargo hold.

Nathan had fired up the cloning machines and had set them to work, Mutons were first of the which were filed away to be deployed later.

He had then switched the machines to create Sectoids before proceeding to the bridge, Xirrra followed.

"She gave me an army…. And a ship…. I need to contact central…"

Nathan said before Xirrra grabbed at him with her tail, he turned to face her.

"If we have an army, we should use it…. The Elders want us to talk to your officer…. So, he could be hunted down…"

Xirrra said as Nathan nodded, they did have a ship… And the means to make a fighting force able to challenge the Elders.

"Then let us get on with this show…."

Nathan said, the ship would need a name though, the _Avenger_ fit Bradford and his men… He wanted something that the Elders would know and fear.

He could think of no better name then _Harbinger_.

 **(20 minutes later.)**

20 Sectoids and 50 Mutons, that was the current state of Nathan's army, he had found a few Alien Scout Ships aboard the _Harbinger_ , Nathan wondered just how far back the doctor was planning.

Nathan looked back at Xirrra from his point at the controls, the remaining Sectoids to crew the ship.

"I will need… Dna from the other species to create an army…. We will also need scientists…. Engineers."

Nathan said, Xirrra was silent, she would be going against the Elders and their empire…. But they had lied to her, she would help till she found out the truth.

"I know one such base…. Drop the troops we have…. We can handle the rest…"

Xirrra said, Nathan grunted but nodded.

 **(Forests of Europe, 10 minutes later)**

There were dozens of outposts around the former X-Com base… Nathan made sure to deploy 30 of the Mutons and 10 of the Sectoids…. He also had descended to command the force himself…. Arming himself with a Scattergun.

"Blasted…. Sssssnake…"

Nathan said as he and his squad advanced on the base, there was a train full of captive humans all of which were scientists or engineers… Along with supplies.

Nathan had a simple plan, he and his group would capture the train, kill any aliens or ADVENT troops, and then bring them back to _Harbinger_ , and bring all the supplies back with them.

"Kill…"

Nathan said as he slithered behind a box, Xirrra and the remaining troops were in charge of the _Harbinger_ … Nathan liked the cloning machine, it would help him build an army quickly…

Nathan spotted a squad of ADVENT Troopers with a Captain leading them.

Nathan pointed to the troopers while he opened his mouth, he had seen Vipers fire their tongues out and wrap around enemies.

His tongue did indeed do so, the ADVENT Captain was dragged towards Nathan before he cursed the throat of the officer while his Mutons aimed their Beam Rifles at the patrol.

"Say hello to the Elders…."

Nathan hissed as his Mutons fired.

 **(2 minutes later.)**

The Sectoid moved the rest of the 6-man patrol onto the ADVENT dropship the group had controlled.

"Xirrra… I am sending a group of ADVENTS to the _Harbinger_ …. Put them in the cargo hold... We're have an army soon enough…"

Nathan said as the dropship flew off, Nathan turned his attention to the train, there was a group of ADVENT Troopers, a squad of MECs which Nathan guessed were part of the train's cargo.

He scanned through the rest of the alien and ADVENT troops, making note of any detail he could use to win the battle.

There was 2 Archons, Nathan knew they were commanders for the aliens… He would make sure to target them first so they were off balanced.

There were a few soldiers with black and green armor which Nathan didn't remember.

There was Sectoids… Of course, they couldn't skimp on soldiers, they were a global empire.

There was a squad or two of Mutons, Nathan couldn't tell if they were here for reinforcement or if the ADVENT troopers were there to reinforce their army.

And then there was something that made Nathan curse… Vipers, he knew Xirrra would be watching, he couldn't kill them…. He didn't want to kill anyone he didn't have to…. But he would have to if he had to.

"Xirrra…. Do you…."

Nathan asked only to hear a his as he motioned for 8 Mutons and 4 Sectoids to move up, he would need a bigger force to deal with this base.

That was when the explosions started to happen, ripping the street up.

"What…...?"

Nathan asked as Resistance soldiers came out to attack the train…. He was surprised.

 **Author Notes**

 **Phew, another chapter done! Yes, it was a short chapter and I know the cloning machine is a stretch… I will explain it next chapter… Next chapter will be not next week, but the week after that and will show Nathan and his troops fighting the Elders and their army to grow their forces. Until then, Lighting Wolf out!**


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